Advanced diesel combustion is of great interest due to its promise Of simultaneously reducing emissions Of nitrogen oxides (NOx) and particulate matter (PM), while maintaining or improving efficiency. However, the extended ignition delay along with the combustion of a Partially premixed charge results in excessive emissions from incomplete combustion, specifically total hydrocarbons (THC) and carbon monoxide (CO). In this study, a light-duty turbodiesel engine was operated in an advanced diesel combustion mode, specifically high efficiency clean combustion (HECC), using three different fuels including a conventional ultralow sulfur diesel fuel (diesel), a synthetic fuel produced in a high temperature Fischer-Tropsch (HTFT) process, and a synthetic fuel produced in a low temperature Fischer-Tropsch (LTFT) process. Start of injection (SOT) timing was swept from -8 degrees ATDC to 0 degrees ATDC to find the optimized injection timing for each fuel; The HTFT fuel, which had a derived cetane number. (DON) of 51, was found to decrease THC and CO emission by 32% and 31%, respectively, compared to the diesel fuel which had a DCN of 45. The higher ignition quality of the HTFT fuel was found to reduce emission from incomplete combustion by presumably consuming more of the fuel charge before it reached a region of the cylinder where it was too lean to effectively burn. However, with the HTFT fuel, NOx and PM emissions increased relative to the diesel baseline due to a higher peak heat release rate, presumably caused by 2% less EGR during the HTFT fuel's operation In contrast, the LTFT :Fuel with a DCN of 81 enabled an 80% reduction in THC emissions and a 74% reduction in CO emissions compared to the diesel fuel. The LTFT fuel, though having a very short, ignition delay, did not increase NOx and PM emissions apparently due to the fuel burning in a shorter, less intense premixed combustion phase followed by a prominent mixing controlled combustion phase. This study revealed that a high ignition quality (DCN 81) fuel is well suited for operation under a high EGR advanced diesel mode and led to reductions in all primary pollutant emissions.